User blog comment:Sefiros2211/Dante's Age/@comment-775152-20121207061630/@comment-775152-20121209012710

Canonically speaking, Vergil is presumed dead, yes. But some fans (myself included) like to entertain the thought that some event, which we are not yet privy to, happens, and as a result of said event, Vergil returns to the human world. For whatever reason you'd like to assign to it, he puts on Dante's colors and is mistaken for Dante otherwise pretends to be Dante.

If you notice, in the cutscene where you defeat Nelo Angelo for the final time, a gout of purple smoke is created, just as with previous encounters when he runs away. Some people assume that this means he, or some part of him, escaped the fight, and was able to return later.

This is, of course, all fan speculation. And it is fun to speculate!